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The Nucleosome

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...

The Nucleosome

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

Chromatin Packaging

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter?
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.

Chromatin Packaging

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...

DNA as a Genetic Template

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

DNA as a Genetic Template

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

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Related Experiment Video

Updated: Jun 16, 2026

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

How stiff is DNA?

Guohui Zheng¹, Luke Czapla, A R Srinivasan

¹Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.

Physical Chemistry Chemical Physics : PCCP

|February 2, 2010

Summary

This summary is machine-generated.

New simulations reveal DNA's natural stiffness is key for biological processes and nanotechnology. The study models DNA's flexibility, crucial for understanding its behavior in confined spaces and designing molecular devices.

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Area of Science:

Biophysics
Nanotechnology
Computational Biology

Background:

DNA's inherent stiffness influences protein interactions, biological processing, and packaging.
This mechanical property is also vital for applications in nanotechnology, including molecular devices and nanomaterials.

Purpose of the Study:

To investigate the behavior of deformable DNA molecules using Monte Carlo simulations.
To understand DNA's behavior in confined cellular environments and aid in designing novel nanomaterials.
To analyze the impact of molecular probes and their tethers on DNA chain extension.

Main Methods:

Utilized Monte Carlo simulations to model deformable DNA molecules.
Compared the conventional elastic-rod representation with more realistic models considering base-pair step deformability.
Analyzed the end-to-end extension fluctuations and their variance with chain length.
Investigated the influence of chemical linkages and molecular probes on DNA chain extension.

Main Results:

End-to-end distance variance increases quadratically with chain length for short DNA chains.
The presence of molecular probes affects end-to-end variance, dependent on chain length, even with rigid connections.
The elastic rod model combined with a fluctuating tether accurately reproduces experimental data from small-angle X-ray scattering.

Conclusions:

The elastic rod model provides a satisfactory explanation for DNA end-to-end distance distributions.
Additional structural fluctuations are not necessary to explain experimental observations of DNA flexibility.
Simulations offer valuable insights for both biological understanding and nanotechnology design involving DNA.